crossing96/oncoscreening huggingface dataset:
NBI - plasma vaporization hybrid approach in bladder cancer endoscopic management.	OBJECTIVES: A prospective study was performed aiming to evaluate the surgical efficacy, perioperative safety profile, diagnostic accuracy and medium term results of a multi-modal approach consisting in narrow band imaging (NBI) cystoscopy and bipolar plasma vaporization (BPV) when compared to the standard protocol represented by white light cystoscopy (WLC) and transurethral resection of bladder tumors (TURBT). MATERIALS & METHODS: A total of 260 patients with apparently at least one bladder tumor over 3 cm were included in the trial. In the first group, 130 patients underwent conventional and NBI cystoscopy followed by BPV, while in a similar number of cases of the second arm, classical WLC and TURBT were applied. In all non-muscle invasive bladder tumors' (NMIBT) pathologically confirmed cases, standard monopolar Re-TUR was performed at 4-6 weeks after the initial intervention, followed by one year' BCG immunotherapy. The follow-up protocol included abdominal ultrasound, urinary cytology and WLC, performed every 3 months for a period of 2 years. RESULTS: The obturator nerve stimulation, bladder wall perforation, mean hemoglobin level drop, postoperative bleeding, catheterization period and hospital stay were significantly reduced for the plasma vaporization technique by comparison to conventional resection. Concerning tumoral detection, the present data confirmed the NBI superiority when compared to standard WLC regardless of tumor stage (95.3% vs. 65.1% for CIS, 93.3% vs. 82.2% for pTa, 97.4% vs. 94% for pT1, 95% vs. 84.2% overall). During standard Re-TUR the overall (6.3% versus 17.4%) and primary site (3.6% versus 12.8%) residual tumors' rates were significantly lower for the NBI-BPV group. The 1 (7.2% versus 18.3%) and 2 (11.5% versus 25.8%) years' recurrence rates were substantially lower for the combined approach. CONCLUSIONS: NBI cystoscopy significantly improved diagnostic accuracy, while bipolar technology showed a higher surgical efficiency, lower morbidity and faster postoperative recovery. The combined technique offered a reduced rate of residual tumors at Re-TUR, both globally as well as for orthotopic tumors. Substantially lower recurrence rates were found at 1 and 2 years among the NBI-BPV cases.	bladder
Global gene expression profiling identifies ALDH2, CCNE1 and SMAD3 as potential prognostic markers in upper tract urothelial carcinoma.	BACKGROUND: Current knowledge about the molecular properties and prognostic markers of upper tract urothelial carcinoma (UTUC) is sparse and often based on bladder urothelial carcinoma (UC), which is thought to share common risk factors with UTUC. However, studies have suggested that differences exist regarding tumor behavior and molecular biology of these cancers, comprehensive investigations are needed to guide the clinical management of UTUC. In recent years, massively parallel sequencing has allowed insights into the biology of many cancers, and molecular prognostic markers based on this approach are rapidly emerging. The goal of this study was to characterize the gene expression patterns of UTUC using massively parallel sequencing, and identify potential molecular markers for prognosis in patients with UTUC. METHODS: We compared the genome-wide mRNA expression profile of cancer and matched normal tissues from 10 patients with UTUC to identify significantly deregulated genes. We also examined the protein levels of prognostic marker candidates in 103 patients with UTUC, and tested the association of these markers with overall survival using Kaplan-Meier model and Cox regression. RESULTS: Functional enrichment of significantly deregulated genes revealed that expression patterns of UTUC were characterized by disorders of cell proliferation and metabolism. And we also compared the expression profile of UTUC with that of bladder UC. Our results highlighted both shared (e.g. disorders of cell cycling and growth signal transduction) and tumor-specific (e.g. abnormal metabolism in UTUC and disruptions of adhesion pathways in bladder UC) features of these two cancers. Importantly, we identified that low protein expression of ALDH2 while high CCNE1 and SMAD3 were significantly associated with increased depth (*P <0.05) and lower overall survival (***P <0.0001) in an independent set of 103 patients. Multivariate Cox regression revealed that all these three genes were independent prognostic indicators in patients with UTUC (***P <0.001). CONCLUSIONS: In conclusion, our study characterized the comprehensive expression profile of UTUC and highlighted both commons and differences in expression patterns between UTUC and bladder UC. And we, for the first time, revealed that ALDH2, CCNE1 and SMAD3 are associated with prognosis in patients with UTUC.	bladder
Epistasis analysis using multifactor dimensionality reduction.	Here we introduce the multifactor dimensionality reduction (MDR) methodology and software package for detecting and characterizing epistasis in genetic association studies. We provide a general overview of the method and then highlight some of the key functions of the open-source MDR software package that is freely distributed. We end with a few examples of published studies of complex human diseases that have used MDR.	bladder
Schwannoma of the urinary bladder: a case report.	Bladder schwannomas are exceedingly rare, benign or malignant, nerve sheath tumors that are most often discovered in patients with a known diagnosis of Neurofibromatosis type 1 (NF1). A few sporadic case reports of bladder schwannoma have been published in urologic, obstetric/gynecologic, and pathologic journals. We report a case of an isolated schwannoma of the urinary bladder. To our knowledge, this represents only the sixth case of benign schwannoma of the urinary bladder in a patient without von Recklinghausen disease.	bladder
Simultaneous radical nephroureterectomy and transurethral distal ureter balloon occlusion and detachment.	BACKGROUND: Distal ureter bladder cuff (DUBC) excision is an essential part of radical nephroureterectomy (RNU) but there is no agreement on the ideal surgical technique to achieve it. We describe a novel technique for endoscopic DUBC excision during RNU that complies with the oncological principle of preventing spillage of tumor cells, by occluding the distal ureter before its excision, while shortening surgical time, and by avoiding repositioning the patient. METHODS: Between June 2010 and May 2012, 10 patients underwent simultaneous open RNU and transurethral distal ureter balloon occlusion and detachment using a flexible cystoscope (f-TUDUBOD) in lumbotomy position. After having ruled out the presence of a concomitant bladder tumor, one surgeon used a flexible cystoscope to occlude the affected ureter with a 5Fr Fogarty catheter and circumferentially incised the orifice until detaching it from the bladder with a boogie electrode or a Holmium laser; meanwhile, two other surgeons performed open RNU through a lumbotomic approach. Data were compared with those of patients who had previously undergone open RNU after TUDUBOD. RESULTS: Mean surgical time for simultaneous open RNU and f-TUDUBOD was 113.4±29.2 minutes, significantly shorter (P<0.01) than that for open RNU after TUDUBOD (154.2±26.4 minutes). There were no complications. Surgical margins were always negative; at mean follow-up of 31.1 months, there was no recurrence in the perivesical space and a 20% (2/10) bladder recurrence rate comparing favorably with that (23.1%) observed at 30-month follow-up in patients who had undergone open RNU after TUDUBOD. CONCLUSIONS: Simultaneous open RNU and f-TUDUBOD proved to be feasible and to represent a safe and effective means of shortening surgical time, with obvious clinical and economical benefits.	bladder
Bacillus Calmette-Guérin (BCG) infection following intravesical BCG administration as adjunctive therapy for bladder cancer: incidence, risk factors, and outcome in a single-institution series and review of the literature.	Bacillus Calmette-Guérin (BCG) is the most effective intravesical immunotherapy for superficial bladder cancer. Although generally well tolerated, BCG-related infectious complications may occur following instillation. Much of the current knowledge about this complication comes from single case reports, with heterogeneous diagnostic and therapeutic approaches and no investigation on risk factors for its occurrence. We retrospectively analyzed 256 patients treated with intravesical BCG in our institution during a 6-year period, with a minimum follow-up of 6 months after the last instillation. We also conducted a comprehensive review and pooled analysis of additional cases reported in the literature since 1975. Eleven patients (4.3%) developed systemic BCG infection in our institution, with miliary tuberculosis as the most common form (6 cases). A 3-drug antituberculosis regimen was initiated in all but 1 patient, with a favorable outcome in 9/10 cases. There were no significant differences in the mean number of transurethral resections prior to the first instillation, the time interval between both procedures, the overall mean number of instillations, or the presence of underlying immunosuppression between patients with or without BCG infection. We included 282 patients in the pooled analysis (271 from the literature and 11 from our institution). Disseminated (34.4%), genitourinary (23.4%), and osteomuscular (19.9%) infections were the most common presentations of disease. Specimens for microbiologic diagnosis were obtained in 87.2% of cases, and the diagnostic performances for acid-fast staining, conventional culture, and polymerase chain reaction (PCR)-based assays were 25.3%, 40.9%, and 41.8%, respectively. Most patients (82.5%) received antituberculosis therapy for a median of 6.0 (interquartile range: 4.0-9.0) months. Patients with disseminated infection more commonly received antituberculosis therapy and adjuvant corticosteroids, whereas those with reactive arthritis were frequently treated only with nonsteroidal antiinflammatory drugs (p < 0.001 for all comparisons). Attributable mortality was higher for patients aged ≥65 years (7.4% vs 2.1%; p = 0.091) and those with disseminated infection (9.9% vs 3.0%; p = 0.040) and vascular involvement (16.7% vs 4.6%; p = 0.064). The scheduled BCG regimen was resumed in only 2 of 36 patients with available data (5.6%), with an uneventful outcome. In the absence of an apparent predictor of the development of disseminated BCG infection after intravesical therapy, and considering the protean variety of clinical manifestations, it is essential to keep a high index of suspicion to initiate adequate therapy promptly and to evaluate carefully the risk-benefit balance of resuming intravesical BCG immunotherapy.	bladder
[A case of lymphoepithelioma-like carcinoma of the bladder].	Lymphoepithelioma-like carcinoma (LELC) of the bladder is very rare and only a few cases have been reported so far. Here, we report a case of LELC of the bladder with distant metastasis. A 73-year-old man presented with macroscopic hematuria and miction pain. Cystoscopy revealed non-papillary tumor and tissue biopsy was performed. Histopathological examination showed pure type of LELC in the bladder. Fludeoxyglucose positron emission tomography revealed lymph node metastasis. The tumor progressed rapidly and the patient died 4 months later. Although the prognosis of pure type of LELC has been reported to be good, our case indicates that the prognosis of pure type with distant metastasis may be poor.	bladder
Validation of a coding algorithm to identify bladder cancer and distinguish stage in an electronic medical records database.	Studies on outcomes in bladder cancer rely on accurate methods to identify patients with bladder cancer and differentiate bladder cancer stage. Medical record and administrative databases are increasingly used to study cancer incidence, but few have distinguished cancer stage, and none have focused on bladder cancer. In this study, we used data from The UK Health Improvement Network (THIN) to identify patients with bladder cancer using at least one diagnostic code for bladder cancer, and distinguish muscle-invasive from non-invasive disease using a subsequent code for cystectomy. Algorithms were validated against a gold standard of physician-completed questionnaires, pathology reports, and consultant letters. Algorithm performance was evaluated by measuring positive predictive value (PPV) and corresponding 95% confidence interval (CI). Among all patients coded with bladder cancer (n = 194), PPV for any bladder cancer was 99.5% (95% CI, 97.2-99.9). PPV for incident bladder cancer was 93.8% (95% CI, 89.4-96.7). PPV for muscle-invasive bladder cancer was 70.1% (95% CI, 59.4-79.5) in patients with cystectomy (n = 95) and 83.9% (95% CI, 66.3-94.5) in those with cystectomy plus additional codes for metastases and death (n = 31). Using our codes for bladder cancer, the age- and sex-standardized incidence rate (SIR) of bladder cancer in THIN approximated that measured by cancer registries (SIR within 20%), suggesting that sensitivity was high as well. THIN is a valid and novel database for the study of bladder cancer. Our algorithm can be used to examine the epidemiology of muscle-invasive bladder cancer or outcomes following cystectomy for patients with muscle invasion.	bladder
Accuracy and risk of malignancy for diagnostic categories in urine cytology at a large tertiary institution.	BACKGROUND: At a high-volume center, it became necessary to provide benchmarks for the accuracy and risk of malignancy per urine cytology diagnostic category. The additive sensitivity for the determination of the residual risk of disease was calculated with the goal of determining the performance of cytology and optimal triage, including the number of urine samples, before the detection of malignancy in surveillance patients. METHODS: A 2-year laboratory information system-based search was conducted, and it yielded 587 subjects (695 biopsy and cytology pairs) with histological follow-up. The sensitivity and specificity of cytology for urothelial malignancy, the risk of malignancy per diagnostic category, the additive sensitivity, and the time for conversion from a negative initial cytology result to a positive cytology result were examined. RESULTS: The overall average sensitivity and specificity of cytology were 48.9% and 83.0%, respectively. The additive sensitivity increased with each subsequent cytology and peaked with the third cytology. A median conversion time of 22.2 months from a negative initial cytology result to a positive cytology result and a decline in predictive positive cytology after the fourth cytology were noted. Subcategorization of the atypical category failed to show statistical significance in predicting outcomes of biopsy. Surveillance subjects, as compared to primary subjects, showed a higher sensitivity for the detection of high and low grade cancers. CONCLUSIONS: The findings suggest that atypia favoring malignancy is being appropriately flagged. However, further definition of the atypical category is needed to increase specificity with a better qualitative or quantitative morphological algorithm. This study provides a risk of malignancy for each category for benchmarking and clinical triage. The data suggest that follow-up should include at least 4 consecutive urine specimens over a period of 22.2 months.	bladder
Cancer survivors' disclosure of complementary health approaches to physicians: the role of patient-centered communication.	BACKGROUND: Cancer survivors' disclosure of complementary health approaches (CHAs) to their follow-up care physicians is necessary to ensure the safe and optimal use of such approaches. Rates of disclosure of CHAs are variable and may be facilitated by patient-centered communication. METHODS: This cross-sectional study conducted in 2003-2004 examined a population-based sample of leukemia, colorectal, and bladder cancer survivors (n=623) who were 2 to 5 years after their diagnosis. A subset of participants who reported using CHAs (n=196) was analyzed with multivariate logistic regression to examine the association between patients' perceptions of their physician's patient-centered communication (ie, information exchange, affective behavior, knowledge of patients as persons) and patients' disclosure of CHA use to their physician with adjustments for physician, patient, and patient-physician relationship factors. RESULTS: Thirty-one percent of the full sample used CHAs, and 47.6% of CHA users disclosed their use to their physicians. Disclosure was significantly associated with patient-centered communication even with adjustments for hypothesized covariates (odds ratio [OR], 1.37; 95% confidence interval [CI], 1.09-1.71). Perceived physician knowledge of the patient as a person (OR, 1.28; 95% CI, 1.10-1.48) and information exchange (OR, 1.27; 95% CI, 1.02-1.60) were the aspects of patient-centered communication that contributed to this association. The main reason for nondisclosure assessed in the survey was that survivors did not think that it was important to discuss CHAs (67.0%). A majority of physicians encouraged continued use of CHAs when they were disclosed (64.8%). CONCLUSIONS: Results support the idea that improving the overall patient centeredness of cancer follow-up care and improving the disclosure of CHA use are potentially synergistic clinical goals.	bladder
Multiple mechanisms mediate resistance to sorafenib in urothelial cancer.	Genetic and epigenetic changes in the mitogen activated protein kinase (MAPK) signaling render urothelial cancer a potential target for tyrosine kinase inhibitor (TKI) treatment. However, clinical trials of several TKIs failed to prove efficacy. In this context, we investigated changes in MAPK signaling activity, downstream apoptotic regulators and changes in cell cycle distribution in different urothelial cancer cell lines (UCCs) upon treatment with the multikinase inhibitor sorafenib. None of the classical sorafenib targets (vascular endothelial growth factor receptor 1/-receptor 2, VEGFR1/-R2; platelet-derived growth factor receptor α/-receptor β, PDGFR-α/-β; c-KIT) was expressed at significant levels leaving RAF proteins as its likely molecular target. Low sorafenib concentrations paradoxically increased cell viability, whereas higher concentrations induced G1 arrest and eventually apoptosis. MAPK signaling remained partly active after sorafenib treatment, especially in T24 cells with an oncogenic HRAS mutation. AKT phosphorylation was increased, suggesting compensatory activation of the phosphatidylinositol-3-kinase (PI3K) pathway. Sorafenib regularly down regulated the anti-apoptotic myeloid cell leukemia 1 (Mcl-1) protein, but combinatorial treatment with ABT-737 targeting other B-cell lymphoma 2 (Bcl-2) family proteins did not result in synergistic effects. In summary, efficacy of sorafenib in urothelial cancer cell lines appears hampered by limited effects on MAPK signaling, crosstalk with further cancer pathways and an anti-apoptotic state of UCCs. These observations may account for the lack of efficacy of sorafenib in clinical trials and should be considered more broadly in the development of signaling pathway inhibitors for drug therapy in urothelial carcinoma.	bladder
Medical follow-up for workers exposed to bladder carcinogens: the French evidence-based and pragmatic statement.	BACKGROUND: The aim of this work was to establish recommendations for the medical follow-up of workers currently or previously exposed to carcinogenic substances for the bladder. METHODS: A critical synthesis of the literature was conducted. Sectors of activity where workers are or were exposed to carcinogenic substances for the bladder were listed and classified according to the level of bladder cancer risk. Performances of techniques available for the targeted screening of bladder cancer were analysed, including a simulation of results among high-risk populations in France. RESULTS: The risk level for the professional group and the latency period between the start of exposure and the natural history of the disease were selected to define a targeted screening protocol. The NMP22BC test, exclusive haematuria testing, and combinations of urine cytology with, respectively, the NMP22BC test and haematuria test, generated an extremely high proportion of false positive results. CONCLUSION: Urine cytology is the test that offers the best specificity. Although poor for all bladder cancer stages and grades combined, its sensitivity is better for high grades, which require early diagnosis since late-stage cancers are of very poor prognosis. These results suggest that urine cytology is currently the only technique suitable for proposal within the context of a first line targeted screening strategy for occupational bladder cancer. An algorithm summarising the recommended medical follow-up for workers currently or previously exposed to carcinogenic substances for the bladder is proposed, based on the level of risk of bladder cancer.	bladder
[Expression of IκBα in bladder cancer cell lines is negatively correlated with epithelial-mesenchymal transition and cell invasion in vitro].	OBJECTIVE: To investigate the expression of inhibitor of nuclear factor κBα (IκBα) in bladder cancer cell lines and its correlation with epithelial-mesenchymal transition (EMT) and invasive potential in vitro. METHODS: The expressions of IκBα, epithelia cadherin (E-cadherin), neuronal cadherin (N-cadherin) and vimentin in human bladder cancer RT4, 5637, 235J, J82 and T24 cell lines were detected by Western blotting. Invasive potential of these cell lines was evaluated by Transwell(TM) assay. In addition, morphological characteristics of those cells were carefully observed under a microscope. RESULTS: RT4 and 5637 cells exhibited epithelial cell morphological features, but 253J, J82 and T24 cells had mesenchymal cell morphological features. E-cadherin was over-expressed in RT4 and 5637 cell lines, but the expressions of vimentin and N-cadherin could not been detected in the two cells. E-cadherin could be detected in 253J cells with a lower expression level; J82 and T24 cells had no expression of E-cadherin; vimentin and N-cadherin were highly expressed in 253J, J82 and T24 cells. Transwell(TM) assay showed higher invasive potential of 253J, J82 and T24 cells than RT4 and 5637 cells in vitro. In addition, RT4 and 5637 cells expressed higher levels of IκBα than 253J, J82 and T24 cells. CONCLUSION: Expression of IκBα in human bladder cancer cells is negatively correlated with EMT and tumor invasion in vitro.	bladder